Relevant bibliographies by topics / N-terminal modification enzymes

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Academic literature on the topic 'N-terminal modification enzymes'

Author: Grafiati
Published: 25 May 2024

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Journal articles on the topic "N-terminal modification enzymes"

1

Nakano, Miyako, Sushil K. Mishra, Yuko Tokoro, Keiko Sato, Kazuki Nakajima, Yoshiki Yamaguchi, Naoyuki Taniguchi, and Yasuhiko Kizuka. "Bisecting GlcNAc Is a General Suppressor of Terminal Modification of N-glycan." Molecular & Cellular Proteomics 18, no. 10 (August 2, 2019): 2044–57. http://dx.doi.org/10.1074/mcp.ra119.001534.

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Glycoproteins are decorated with complex glycans for protein functions. However, regulation mechanisms of complex glycan biosynthesis are largely unclear. Here we found that bisecting GlcNAc, a branching sugar residue in N-glycan, suppresses the biosynthesis of various types of terminal epitopes in N-glycans, including fucose, sialic acid and human natural killer-1. Expression of these epitopes in N-glycan was elevated in mice lacking the biosynthetic enzyme of bisecting GlcNAc, GnT-III, and was conversely suppressed by GnT-III overexpression in cells. Many glycosyltransferases for N-glycan terminals were revealed to prefer a nonbisected N-glycan as a substrate to its bisected counterpart, whereas no up-regulation of their mRNAs was found. This indicates that the elevated expression of the terminal N-glycan epitopes in GnT-III-deficient mice is attributed to the substrate specificity of the biosynthetic enzymes. Molecular dynamics simulations further confirmed that nonbisected glycans were preferentially accepted by those glycosyltransferases. These findings unveil a new regulation mechanism of protein N-glycosylation.
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Sakato-Antoku, Miho, Jeremy L. Balsbaugh, and Stephen M. King. "N-Terminal Processing and Modification of Ciliary Dyneins." Cells 12, no. 20 (October 20, 2023): 2492. http://dx.doi.org/10.3390/cells12202492.

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Axonemal dyneins are highly complex microtubule motors that power ciliary motility. These multi-subunit enzymes are assembled at dedicated sites within the cytoplasm. At least nineteen cytosolic factors are specifically needed to generate dynein holoenzymes and/or for their trafficking to the growing cilium. Many proteins are subject to N-terminal processing and acetylation, which can generate degrons subject to the AcN-end rule, alter N-terminal electrostatics, generate new binding interfaces, and affect subunit stoichiometry through targeted degradation. Here, we have used mass spectrometry of cilia samples and electrophoretically purified dynein heavy chains from Chlamydomonas to define their N-terminal processing; we also detail the N-terminal acetylase complexes present in this organism. We identify four classes of dynein heavy chain based on their processing pathways by two distinct acetylases, one of which is dependent on methionine aminopeptidase activity. In addition, we find that one component of both the outer dynein arm intermediate/light chain subcomplex and the docking complex is processed to yield an unmodified Pro residue, which may provide a setpoint to direct the cytosolic stoichiometry of other dynein complex subunits that contain N-terminal degrons. Thus, we identify and describe an additional level of processing and complexity in the pathways leading to axonemal dynein formation in cytoplasm.
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STOUGHTON, Daniel M., Gerardo ZAPATA, Robert PICONE, and Willie F. VANN. "Identification of Arg-12 in the active site of Escherichia coli K1 CMP-sialic acid synthetase." Biochemical Journal 343, no. 2 (October 8, 1999): 397–402. http://dx.doi.org/10.1042/bj3430397.

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Escherichia coli K1 CMP-sialic acid synthetase catalyses the synthesis of CMP-sialic acid from CTP and sialic acid. The active site of the 418 amino acid E. coli enzyme was localized to its N-terminal half. The bacterial CMP-sialic acid synthetase enzymes have a conserved motif, IAIIPARXXSKGLXXKN, at their N-termini. Several basic residues have been identified at or near the active site of the E. coli enzyme by chemical modification and site-directed mutagenesis. Only one of the lysines in the N-terminal motif, Lys-21, appears to be essential for activity. Mutation of Lys-21 in the N-terminal motif results in an inactive enzyme. Furthermore, Arg-12 of the N-terminal motif appears to be an active-site residue, based on the following evidence. Substituting Arg-12 with glycine or alanine resulted in inactive enzymes, indicating that this residue is required for enzymic activity. The Arg-12 → Lys mutant was partially active, demonstrating that a positive charge is required at this site. Steady-state kinetic analysis reveals changes in kcat, Km and Ks for CTP, which implicates Arg-12 in catalysis and substrate binding.
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Roll-Mecak, Antonina, Agnieszka Szyk, and Vasilisa Kormendi. "Microtubule chemical complexity: mechanism of tubulin modification enzymes." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1286. http://dx.doi.org/10.1107/s2053273314087130.

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Tubulin is subject to an abundant and diverse set of post-translational modifications that include phosphorylation, acetylation, poly-glutamylation, poly-glycylation and tyrosination. The highest density and variety of post-translational modifications are found in especially complex microtubule arrays like those of neurons or cilia. Not surprisingly, tubulin modification enzymes have been linked to human diseases including cancers and neurodegenerative disorders. I will present recent data from my lab on the mechanism of action of two tubulin modification enzymes that illustrate two divergent paradigms of tubulin recognition. Tubulin tyrosine ligase (TTL) adds a C-terminal Tyr to the exposed C-terminus of alpha-tubulin as part of a tyrosination/detyrosination cycle present in most eukaryotic cells. We solved the first crystal structure of tubulin tyrosine ligase that revealed how the TTL scaffold supported the expansion of the repertory of tubulin post-translational modification enzymes of the TTL like family that recognize either alpha- or beta-tubulin C-terminal tails. In addition to modifying tubulin, TTL also prevents tubulin from incorporating into microtubules by recognizing a tubulin dimer interface that would otherwise be involved in microtubule lattice interactions. I will also present recent work from my group on the structure and mechanism of action of tubulin acetyltransferase (TAT). TAT acetylates Lys-40 on alpha-tubulin in the microtubule lumen. We solved the 2.7Å structure of TAT bound to its ac-coA substrate as well as the 2.45Å structure of a catalytic inactive TAT mutant that reveals a domain swapped dimer in which the functionally essential N-terminus shows evidence of unprecedented structural plasticity. Implications for catalysis and microtubule stimulation of TAT activity will be discussed.
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Lubelski, Jacek, Wout Overkamp, Leon D. Kluskens, Gert N. Moll, and Oscar P. Kuipers. "Influence of Shifting Positions of Ser, Thr, and Cys Residues in Prenisin on the Efficiency of Modification Reactions and on the Antimicrobial Activities of the Modified Prepeptides." Applied and Environmental Microbiology 74, no. 15 (June 6, 2008): 4680–85. http://dx.doi.org/10.1128/aem.00112-08.

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ABSTRACT Since the recent discovery that the nisin modification and transport machinery can be used to produce and modify peptides unrelated to nisin, specific questions arose concerning the specificity of the modification enzymes involved and the limits of their promiscuity with respect to the dehydration and cyclization processes. The nisin leader peptide has been postulated to fulfill a recognition and binding function required for these modifications. Here, we investigated whether the relative positions of the modifiable residues in the nisin prepeptide, with respect to the leader peptide, could influence the efficiency of their modification. We conducted a systematic study on the insertion of one to four alanines in front of either ring A or ring D to change the “reading frame” of modifiable residues, resulting in altered distance and topology of the modifiable residues relative to the leader. The insertion of N-terminal and hinge-located Ala residues had only a modest influence on the modification efficiency, demonstrating that the “phasing” of these residues relative to the leader peptide is not a critical factor in determining modification. However, in all cases, but especially with the N-terminal insertions, the antimicrobial activities of the fully modified nisin species were decreased.
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Nakonieczna, Joanna, Tadeusz Kaczorowski, Agnieszka Obarska-Kosinska, and Janusz M. Bujnicki. "Functional Analysis of MmeI from Methanol Utilizer Methylophilus methylotrophus, a Subtype IIC Restriction-Modification Enzyme Related to Type I Enzymes." Applied and Environmental Microbiology 75, no. 1 (November 7, 2008): 212–23. http://dx.doi.org/10.1128/aem.01322-08.

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ABSTRACT MmeI from Methylophilus methylotrophus belongs to the type II restriction-modification enzymes. It recognizes an asymmetric DNA sequence, 5′-TCCRAC-3′ (R indicates G or A), and cuts both strands at fixed positions downstream of the specific site. This particular feature has been exploited in transcript profiling of complex genomes (using serial analysis of gene expression technology). We have shown previously that the endonucleolytic activity of MmeI is strongly dependent on the presence of S-adenosyl-l-methionine (J. Nakonieczna, J. W. Zmijewski, B. Banecki, and A. J. Podhajska, Mol. Biotechnol. 37:127-135, 2007), which puts MmeI in subtype IIG. The same cofactor is used by MmeI as a methyl group donor for modification of an adenine in the upper strand of the recognition site to N 6-methyladenine. Both enzymatic activities reside in a single polypeptide (919 amino acids [aa]), which puts MmeI also in subtype IIC of the restriction-modification systems. Based on a molecular model, generated with the use of bioinformatic tools and validated by site-directed mutagenesis, we were able to localize three functional domains in the structure of the MmeI enzyme: (i) the N-terminal portion containing the endonucleolytic domain with the catalytic Mg2+-binding motif D70-X9-EXK82, characteristic for the PD-(D/E)XK superfamily of nucleases; (ii) a central portion (aa 310 to 610) containing nine sequence motifs conserved among N 6-adenine γ-class DNA methyltransferases; (iii) the C-terminal portion (aa 610 to 919) containing a putative target recognition domain. Interestingly, all three domains showed highest similarity to the corresponding elements of type I enzymes rather than to classical type II enzymes. We have found that MmeI variants deficient in restriction activity (D70A, E80A, and K82A) can bind and methylate specific nucleotide sequence. This suggests that domains of MmeI responsible for DNA restriction and modification can act independently. Moreover, we have shown that a single amino acid residue substitution within the putative target recognition domain (S807A) resulted in a MmeI variant with a higher endonucleolytic activity than the wild-type enzyme.
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Kelley, M., and D. A. Vessey. "Structural comparison between the mitochondrial aralkyl-CoA and arylacetyl-CoA N-acyltransferases." Biochemical Journal 288, no. 1 (November 15, 1992): 315–17. http://dx.doi.org/10.1042/bj2880315.

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The aralkyl and arylacetyl transferases were purified to homogeneity from bovine kidney by a slight modification of a previous procedure. The M(r) of the arylacetyl transferase was estimated to be 33,500 by SDS/PAGE and that of the aralkyl transferase to be 33,750 by a combination of SDS/PAGE and gel-filtration analysis. N-Terminal-sequence analysis indicated a blocked N-terminus for the arylacetyl transferase and gave the following sequence for the aralkyl transferase: M-F-L-L-Q-G-A-Q-M-L-Q-M-L-E-K. Amino acid analysis revealed differences in composition between the two enzymes. Most notable was the fact that the aralkyl transferase had more methionine and leucine. This difference could be partially accounted for by assuming that the methionine-and-leucine-rich N-terminus was missing from the arylacetyl transferase. Chemical cleavage of the two enzymes at methionine residues using CNBr gave rise to several peptides for each enzyme. N-Terminal-sequence analysis of the 8000-M(r) peptide from the arylacetyl transferase gave a sequence with 69% similarity to the 9000-M(r) peptide from the aralkyl transferase. This was taken to indicate a common origin for the two enzymes.
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Smith, Clyde A., Marta Toth, Nichole K. Stewart, Lauren Maltz, and Sergei B. Vakulenko. "Structural basis for the diversity of the mechanism of nucleotide hydrolysis by the aminoglycoside-2′′-phosphotransferases." Acta Crystallographica Section D Structural Biology 75, no. 12 (November 29, 2019): 1129–37. http://dx.doi.org/10.1107/s2059798319015079.

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Aminoglycoside phosphotransferases (APHs) are one of three families of aminoglycoside-modifying enzymes that confer high-level resistance to the aminoglycoside antibiotics via enzymatic modification. This has now rendered many clinically important drugs almost obsolete. The APHs specifically phosphorylate hydroxyl groups on the aminoglycosides using a nucleotide triphosphate as the phosphate donor. The APH(2′′) family comprises four distinct members, isolated primarily from Enterococcus sp., which vary in their substrate specificities and also in their preference for the phosphate donor (ATP or GTP). The structure of the ternary complex of APH(2′′)-IIIa with GDP and kanamycin was solved at 1.34 Å resolution and was compared with substrate-bound structures of APH(2′′)-Ia, APH(2′′)-IIa and APH(2′′)-IVa. In contrast to the case for APH(2′′)-Ia, where it was proposed that the enzyme-mediated hydrolysis of GTP is regulated by conformational changes in its N-terminal domain upon GTP binding, APH(2′′)-IIa, APH(2′′)-IIIa and APH(2′′)-IVa show no such regulatory mechanism, primarily owing to structural differences in the N-terminal domains of these enzymes.
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Caillava, Celine, Jean Sevalle, and Frederic Checler. "P2-219: identification of enzymes involved in n-terminal truncation and modification of amyloid peptide." Alzheimer's & Dementia 7 (July 2011): S382. http://dx.doi.org/10.1016/j.jalz.2011.05.1101.

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Nashed, Salomé, Houssam El Barbry, Médine Benchouaia, Angélie Dijoux-Maréchal, Thierry Delaveau, Nadia Ruiz-Gutierrez, Lucie Gaulier, et al. "Functional mapping of N-terminal residues in the yeast proteome uncovers novel determinants for mitochondrial protein import." PLOS Genetics 19, no. 8 (August 16, 2023): e1010848. http://dx.doi.org/10.1371/journal.pgen.1010848.

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N-terminal ends of polypeptides are critical for the selective co-translational recruitment of N-terminal modification enzymes. However, it is unknown whether specific N-terminal signatures differentially regulate protein fate according to their cellular functions. In this work, we developed an in-silico approach to detect functional preferences in cellular N-terminomes, and identified in S. cerevisiae more than 200 Gene Ontology terms with specific N-terminal signatures. In particular, we discovered that Mitochondrial Targeting Sequences (MTS) show a strong and specific over-representation at position 2 of hydrophobic residues known to define potential substrates of the N-terminal acetyltransferase NatC. We validated mitochondrial precursors as co-translational targets of NatC by selective purification of translating ribosomes, and found that their N-terminal signature is conserved in Saccharomycotina yeasts. Finally, systematic mutagenesis of the position 2 in a prototypal yeast mitochondrial protein confirmed its critical role in mitochondrial protein import. Our work highlights the hydrophobicity of MTS N-terminal residues and their targeting by NatC as important features for the definition of the mitochondrial proteome, providing a molecular explanation for mitochondrial defects observed in yeast or human NatC-depleted cells. Functional mapping of N-terminal residues thus has the potential to support the discovery of novel mechanisms of protein regulation or targeting.
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Dissertations / Theses on the topic "N-terminal modification enzymes"

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Sunde, Margaret. "N-terminal modification of S-adenosylmethionine decarboxylase." Thesis, University of Cambridge, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.318198.

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El, Barbry Houssam. "Découverte du rôle crucial du résidu en position 2 des séquences MTS d’adressage mitochondrial." Electronic Thesis or Diss., Sorbonne université, 2023. http://www.theses.fr/2023SORUS035.

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Les mitochondries sont des organites complexes impliquant un millier de protéines, la plupart codées dans le génome nucléaire. Leur biogenèse a nécessité au cours de l’évolution la mise en place de systèmes efficaces d’adressage et d’import protéique, et des défaillances de ces systèmes sont associées à des pathologies graves, neuropathies, troubles cardiovasculaires, myopathies, maladies neurodégénératives ainsi que cancers. De nombreuses protéines mitochondriales possèdent en N-terminal une séquence d’adressage appelée MTS (Mitochondrial Targeting sequence) qui forme une hélice alpha amphiphile essentielle pour leur import mitochondrial. La séquence des divers MTSs est néanmoins très variables et leur caractéristiques critiques ne sont pas encore bien comprises. Le point de départ de ma thèse est la découverte, chez les levures, d’une surreprésentation en position 2 des séquences MTSs de 4 acides aminés hydrophobes (F, L, I, W). Au cours de mes années de thèse, j’ai pu confirmer, par des expériences de mutagenèse dirigée, le rôle critique de la nature du résidu en position 2 des MTSs. En effet, grâce au développement d’un système novateur de criblage des défauts d’import basé sur le sauvetage fonctionnel de la toxicité d’une protéine mitochondriale, j’ai pu observer que seuls les résidus surreprésentés en position 2 des protéines mitochondriales permettaient un import efficace. Mon travail a ainsi démontré l'existence de fortes contraintes évolutives s’exerçant au niveau de la position 2 des MTSs dont la compréhension pourrait à terme être utile pour optimiser l’adressage mitochondrial de protéines thérapeutiques chez des patients atteints de maladies mitochondriales
Mitochondria are complex organelles involving a thousand proteins, most of which are encoded in the nuclear genome. Their biogenesis has required the evolutionary development of efficient protein addressing and import systems, and failures of these systems are associated with serious pathologies, neuropathies, cardiovascular disorders, myopathies, neurodegenerative diseases and cancers.Many mitochondrial proteins have an N-terminal addressing sequence called MTS (Mitochondrial Targeting Sequence) which forms an amphiphilic alpha helix essential for their mitochondrial import. However, the sequence of the various MTSs is highly variable and their critical characteristics are not yet well understood. The starting point of my thesis was the discovery in yeast of an overrepresentation of 4 hydrophobic amino acids (F, L, I, W) at position 2 of the MTSs sequences. During my thesis, I was able to confirm the critical role of the nature of the residue in position 2 of the MTSs through directed mutagenesis experiments. Indeed, thanks to the development of an innovative system for screening import defects based on the functional rescue of the toxicity of a mitochondrial protein, I was able to observe that only residues overrepresented at position 2 of mitochondrial proteins allowed efficient import. My work has thus demonstrated the existence of strong evolutionary constraints at position 2 of MTSs, the understanding of which could ultimately be useful for optimising the mitochondrial addressing of therapeutic proteins in patients suffering from mitochondrial diseases
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Kshetri, Man B. "N-TERMINAL DOMAIN OF rRNA METHYLTRANSFERASE ENZYME RsmC IS IMPORTANT FOR ITS BINDING TO RNA AND RNA CHAPERON ACTIVITY." Kent State University Honors College / OhioLINK, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=ksuhonors1621007414429417.

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Boisson, Bertrand. "Caractérisation et fonction de la N-myristoylation du protéome d'Arabidopsis thaliana." Paris 6, 2003. http://www.theses.fr/2003PA066367.

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Piontek, Alexander. "Deciphering the Catalytic Mechanism of the Zn Enzyme Glutaminyl Cyclase and the Deduction of Transition-State Analog Inhibitors." Doctoral thesis, 2014. http://hdl.handle.net/11858/00-1735-0000-0022-605A-C.

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Book chapters on the topic "N-terminal modification enzymes"

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Pennings, Sari, Timothy E. O’Neill, Geert Meersseman,, and E. Morton Bradbury. "Nucleosomes: dynamic repressors of transcription." In Nuclear Organization, Chromatin Structure, and Gene Expression, 3–18. Oxford University PressOxford, 1997. http://dx.doi.org/10.1093/oso/9780198549239.003.0001.

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Abstract The structure of the nucleosome, which was elucidated from early work on enzyme digestion patterns, neutron scatter, X-ray diffraction data, and histone— DNA crosslinking (reviewed by Van Bolde 1988), is essentially a static picture of an average structure. This is because these experimental approaches average out the heterogeneities across the largely native bulk nucleosome and chromatin samples, as well as any fluctuations in the structure over time. Most notably, the model of the nucleosome rarely includes the long N-terminal and short C-terminal ‘tails’ of the histones, which are highly dynamic and contain the sites of reversible chemical modifications associated with chromatin functions (reviewed by Bradbury 1992; also see Chapter 3). Studies of higher order structures of chromatin also hold this caveat and here the paucity of data allows for several models of the 30 nm fibril model (reviewed by Van Bolde 1988). However useful these structural models arc in understanding the packaging of chromatin, they fail to convey how chromatin structure can be flexible enough not only to accommodate the wide range of DNA sequences in the genome, but also to allow dynamic processes such as transcription and replication to take place. An insight into the dynamic nature of chromatin is essential in order to understand how chromatin can be a functional component of the active eukaryotic nucleus.
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